I think translucent works. The opaqueness of Wind Waker worked for that game -- if anything to hide the fact that there was a submerged kingdom below. (Although the depth to it wouldn't be visible from the surface, but I digress...) The perfect clarity of TP's water was nice, and gave a great sense of depth, but wasn't too realistic. I never thought about it until this question came up, but a translucent quality to it would be nice.
I suppose it would be a good place to use the distance draw fog that plagued so many older games. Maybe this is why they didn't make the water murky in TP, in order to not get slammed about cheapening out with fog effects. I think a clarity to a certain depth / distance would be nice, and would hopefully be well achieveable in SS.
I really like that Naruto screenshot posted above. That is a style I'd be happy with as well.